Author:

Chatrathip Nasongkla

Mentor:

Wei-Jen Lin, Professor of Microbiology, Cal Poly Pomona

Clostridium botulinum is a spore-forming, Gram-positive bacteria that belong to phylum Firmicutes. It produces botulinum neurotoxin, the most poisonous neurotoxin known to man. The genomes of several Clostridium botulinum strains have been sequenced and annotated, which provides a great tool for mining this bacterial species. Analysis of comparative gaps between Clostridium botulinum Hall A and ATCC 3502 identified interspersed DNA repeats. Repeats have been found throughout eukaryotes and prokaryotes. Previously considered “junk DNA”, these repeats are thought to have stable, secondary RNA structures suggesting their roles in gene expression. This study focuses on a repeat sequence designated “Repeat 1”. Analysis of Repeat 1 sequences identified four subgroups of repeats named 1A, 1B, 1C, and 1D whose size ranges from 34 bp to 240 bp and frequency of each repeat ranges from 5 to 20 sequences per genome. Repeat sequences run in both directions on the genome of Clostridium botulinum ATCC 3502. The sequences of Repeat 1, 1B, and 1C are flanked by direct repeats of TTTAT which also occurred in bcr1-bcr3 repeats of Bacillus cereus. The prevalence and functions of these repeats in Clostridium and closely related bacterial genomes will be further investigated.